1000G And Dbsnp Build 132 In Ucsc Genome Browser?

Question

[Ryan D]

Hello ballers,

So correct me if I'm wrong, but as I understand it all of the pilot3 data from 1000G has been deposited in dbSNP132. 1000G data currently has SNPs in forms like this as well: chr19:50811843 50811843

So two questions: 1. Are these new SNPs without rsID#s going (or already in) dbSNP and if so do they have/rs#s (if not, how to look up?)

1. When will the UCSC genome browser put SNP132 online? Right now the browser has just SNP131.

Thanks and thanks for all of you who tweeted #ASHG2010 Ryan D Twitter: @delahar

Answer 1

[Treylathe]

1. The 1000 Genomes snps should have rs ids. Newly submitted snps have ss IDs first (you can see the 1000 genomes submissions here, these are then computationally clustered with other submissions to create the rs ID. So the answer is yes :) http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch5

2. I believe that some of the 1000 genomes project SNPs are in the genome browser. You can go to the table browser, chose the latest human assembly, chose the 131 build of SNPs and then filter for 1000 Genome validated SNPs in the filter. Might not be all of them, but there are many there. According to UCSC mailing list, it takes 4-6 weeks to update the track to a new build. I think the build was released in late september, so that'd be coming up soon.

Answer 2

[Mary]

Wow, just went to look and realized that all the presentations from the evening tutorial session are up at NHGRI already: http://genome.gov/27542240

There's one whole segment on how to access the data that might have some useful tidbits.

Answer 3

[lh3]

People who are on the 1000 analysis mailing list should know that NCBI has just released a single VCF file for dbSNP132. It is nearly non-redundant. Sources of SNPs (e.g. if found by G1K) are also labeled. Before UCSC readies dbSNP132, I would load this VCF to IGV for viewing.

At the same time, it should be noted that these G1K SNPs were called nearly two years ago (initial pilot calls have been dumped to dbSNP131, I think). Data quality and quantity and SNP calling methods have all been considerably improved since then. If you are looking for a more complete and more accurate call set, come here. This is not a released call set, though.

[Mary]

Is that an open announcement mailing list? I asked them at this ASHG session if there was one, and I was told there wasn't one yet, but that they were setting one up.

[lh3]

No, it is not open.

Answer 4

[Laura]

The is now an official release of snps for the main project

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/2010_11/README.20100804_merged_snp_set

This is more than 25millon snps.

Genotypes for the 629 individuals who were in the analysis set will be released shortly